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- PDB-4uyp: High resolution structure of the third cohesin ScaC in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4uyp
TitleHigh resolution structure of the third cohesin ScaC in complex with the ScaB dockerin with a mutation in the N-terminal helix (IN to SI) from Acetivibrio cellulolyticus displaying a type I interaction.
Components(Cellulosomal scaffoldin ...) x 2
KeywordsCELL ADHESION/PROTEIN BINDING / CELL ADHESION-PROTEIN BINDING COMPLEX / CELLULOSOME / TYPE 1 COHESIN-DOCKERIN INTEREACTIONS / ADAPTOR SCAFFOLDIN SCAB / ANCHORING SCAFFOLDING SCAC
Function / homology
Function and homology information


polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function
: / Type 1 dockerin domain / Dockerin domain / Immunoglobulin-like - #680 / : / Cellulosome anchoring protein, cohesin domain / Cohesin domain / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. ...: / Type 1 dockerin domain / Dockerin domain / Immunoglobulin-like - #680 / : / Cellulosome anchoring protein, cohesin domain / Cohesin domain / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Cellulosomal scaffoldin anchoring protein C / Cellulosomal scaffoldin adaptor protein B
Similarity search - Component
Biological speciesAcetivibrio cellulolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsCameron, K. / Alves, V.D. / Bule, P. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Najmudin, S.
Citation
Journal: J. Biol. Chem. / Year: 2015
Title: Cell-surface Attachment of Bacterial Multienzyme Complexes Involves Highly Dynamic Protein-Protein Anchors.
Authors: Cameron, K. / Najmudin, S. / Alves, V.D. / Bayer, E.A. / Smith, S.P. / Bule, P. / Waller, H. / Ferreira, L.M. / Gilbert, H.J. / Fontes, C.M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Purification, Crystallization and Preliminary X-Ray Characterization of the Acetivibrio Cellulolyticus Type I Cohesin Scac in Complex with the Scab Dockerin.
Authors: Cameron, K. / Alves, V.D. / Bule, P. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Najmudin, S.
History
DepositionSep 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Jun 10, 2015Group: Database references
Revision 1.3Nov 7, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.pdbx_mutation / _entity.src_method / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellulosomal scaffoldin anchoring protein C
B: Cellulosomal scaffoldin adaptor protein B
C: Cellulosomal scaffoldin anchoring protein C
D: Cellulosomal scaffoldin adaptor protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,62230
Polymers49,7894
Non-polymers2,83326
Water11,530640
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10760 Å2
ΔGint-262.5 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.750, 107.750, 100.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Cellulosomal scaffoldin ... , 2 types, 4 molecules ACBD

#1: Protein Cellulosomal scaffoldin anchoring protein C


Mass: 16512.172 Da / Num. of mol.: 2 / Fragment: RESIDUES 326-467
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio cellulolyticus (bacteria) / Gene: scaC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TUNER / References: UniProt: Q7WYN2
#2: Protein Cellulosomal scaffoldin adaptor protein B


Mass: 8382.468 Da / Num. of mol.: 2 / Fragment: RESIDUES 868-942 / Mutation: I822S, N833I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio cellulolyticus (bacteria) / Gene: scaB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TUNER / References: UniProt: Q7WYN3

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Non-polymers , 5 types, 666 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 640 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID (EPE): FROM THE CRYSTALLISATION CONDITION. (4S)- ...4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID (EPE): FROM THE CRYSTALLISATION CONDITION. (4S)-2-METHYL-2,4-PENTANEDIOL (MPD): ROM THE CRYSTALLISATION CONDITION. SULFATE ION (SO4): ROM THE CRYSTALLISATION CONDITION. CALCIUM ION (CA): FROM TEH STORAGE BUFFER.
Sequence detailsTHE THIRD COHESIN CORRESPONDS TO RESIDUES 326 TO 427 OF THE ANCHORING SCAFFOLDIN SCAC. IT HAS A HIS ...THE THIRD COHESIN CORRESPONDS TO RESIDUES 326 TO 427 OF THE ANCHORING SCAFFOLDIN SCAC. IT HAS A HIS TAG AT THE C- TERMINUS. IT IS THE C-TERMINAL DOCKERIN MODULE CORRESPONDING TO RESIDUES 868 TO 942 OF THE ADAPTOR SCAFFOLDIN SCAB.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 7.5
Details: 0.5 M AMMONIUM SULFATE, 0.1 M HEPES PH 7.5, 30%(V/V) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.49→76.19 Å / Num. obs: 96788 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.9
Reflection shellResolution: 1.49→1.53 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.7 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CCL

2ccl


Resolution: 1.49→76.19 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.002 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
RfactorNum. reflection% reflectionSelection details
Rfree0.18536 4843 5 %RANDOM
Rwork0.15548 ---
obs0.15696 91945 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.162 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.49→76.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3345 0 162 640 4147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.023845
X-RAY DIFFRACTIONr_bond_other_d0.0850.023832
X-RAY DIFFRACTIONr_angle_refined_deg2.86725307
X-RAY DIFFRACTIONr_angle_other_deg2.77638656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2645530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15325.337163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96315630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9441512
X-RAY DIFFRACTIONr_chiral_restr0.420.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024339
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02833
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9441.2981853
X-RAY DIFFRACTIONr_mcbond_other1.8871.2961852
X-RAY DIFFRACTIONr_mcangle_it2.8321.932337
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8131.6781992
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 361 -
Rwork0.243 6658 -
obs--98.87 %
Refinement TLS params.Method: refined / Origin x: 8.975 Å / Origin y: -35.2473 Å / Origin z: 6.1908 Å
111213212223313233
T0.0121 Å20.0094 Å2-0.008 Å2-0.0184 Å2-0.003 Å2--0.0087 Å2
L0.0747 °2-0.0356 °2-0.0844 °2-0.0818 °20.0385 °2--0.0958 °2
S-0.0046 Å °-0.0008 Å °0.0085 Å °-0.0038 Å °0.0132 Å °-0.0038 Å °0.0072 Å °0.0029 Å °-0.0086 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 144
2X-RAY DIFFRACTION1B1 - 201
3X-RAY DIFFRACTION1C1 - 146
4X-RAY DIFFRACTION1D1 - 201

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